An enhanced molecular marker based genetic map of perennial ryegrass (<i>Lolium perenne</i>) reveals comparative relationships with other Poaceae genomes

Jones, Elizabeth; Mahoney, Natalia; Hayward, M. D.; Armstead, Ian; Jones, James T. A.; Humphreys, Mervyn O.; King, I. P.; Kishida, T.; Yamada, Toshihiko; Balfourier, François; Charmet, G.; Forster, John W.

doi:10.1139/g01-144

Cited by 210 publications

(264 citation statements)

References 53 publications

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“…Lolium/Festuca and rice is largely consistent with previous report (Jones et al 2002;Alm et al 2003;Sim et al 2005). For example, with a few exceptions, rice chromosome 1 corresponds to Lolium/Festuca chromosome 3 , and rice chromosome 3 corresponds to Lolium/Festuca chromosome 4 (Tables 1 and 2).…”

Section: Species Specificities Of the Markers Within Combinations Of supporting

confidence: 91%

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Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

et al. 2009

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DNA markers able to distinguish species or genera with high specificity are valuable in the identification of introgressed regions in interspecific or intergeneric hybrids.Intergeneric hybridization between the genera of Lolium and Festuca, leading to the reciprocal introgression of chromosomal segments, can produce novel forage grasses with unique combinations of characteristics. To characterize Lolium/Festuca introgressions, novel PCR-based expression sequence tag (EST) markers were developed. These markers were designed around intronic regions which show higher polymorphism than exonic regions. Intronic regions of the grass genes were predicted from the sequenced rice genome. Two hundred and nine primer sets were designed from Lolium/Festuca ESTs that showed high similarity to unique rice genes dispersed uniformly throughout the rice genome. We selected 61 of these primer sets as insertion-deletion (indel)-type markers and 82 primer sets as cleaved amplified polymorphic sequence (CAPS) markers to distinguish between Lolium perenne and Festuca pratensis. Specificity of these markers to each species was evaluated by the genotyping of four cultivars and accessions (32 individuals) of L. perenne and F. pratensis respectively. Evaluation using specificity indices proposed in this study suggested that many indel-type markers had high species specificity to L. perenne and F. pratensis, including 15 markers completely specific to both species. Forty-nine of the CAPS markers completely distinguish between the two species at bulk level.Chromosome mapping of these markers using a Lolium/Festuca substitution line 3 revealed syntenic relationships between Lolium/Festuca and rice largely consistent with previous reports. This intron-based marker system that shows a high level of polymorphisms between species in combination with high species specificity will consequently be a valuable tool in Festulolium breeding. Keywordsintergeneric (interspecific) hybrid -intron polymorphismsinsertion-deletion (indel) -specificity to species -rice genome -comparative genomics

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Section: Species Specificities Of the Markers Within Combinations Of supporting

confidence: 91%

“…Out of 143 intron-flanking EST markers, 107 (74.8%) markers were assigned to one of the 7 Festuca chromosomes (Tables 2 and 3 Lolium/Festuca and rice revealed several syntenic segments largely in agreement with previous reports (Jones et al 2002;Alm et al 2003;Sim et al 2005;King et al 2007). …”

Section: Chromosome Mapping Of Intron-flanking Est Markerssupporting

confidence: 88%

Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

et al. 2009

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“…As a member of the Poaceae clade in the grass phylogeny, orchardgrass has a base chromosome number of seven. Several studies have shown the synteny between rice and the seven-chromosome grass species (Gale and Devos 1998; LaRota and Sorrells 2004; Jones et al 2002a). Within orchardgrass, synteny to other grasses may allow for targeted mapping and association studies.…”

Section: Discussionmentioning

confidence: 99%

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

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“…Comparative mapping was performed as described by Jones et al (2002b). The comparative location of probes in the Triticeae and rice genomes were as reported by Jones et al (2002b) and/or ascertained using the Graingenes (http:/ / grain.jouy.inra.fr/ggpages/) and Gramene (http:/ /www.…”

Section: Comparative Analysismentioning

confidence: 99%

“…In our study, QTL1 is also located on LG2, in the proximity of Xcdo385 (Figure 3). According to Jones et al (2002b), Xcdo385 maps to LG2 in the ILGI mapping population. It is in this genomic region that Dumsday et al (2003) also located SSR markers associated with crown rust resistance.…”

Section: H Muylle Et Almentioning

confidence: 99%

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Muylle¹,

Baert²,

Bockstaele

et al. 2005

Heredity

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Crown rust resistance is an important selection criterion in ryegrass breeding. The disease, caused by the biotrophic fungus Puccinia coronata, causes yield losses and reduced quality. In this study, we used linkage mapping and QTL analysis to unravel the genomic organization of crown rust resistance in a Lolium perenne population. The progeny of a pair cross between a susceptible and a resistant plant were analysed for crown rust resistance. A linkage map, consisting of 227 loci (AFLP, SSR, RFLP and STS) and spanning 744 cM, was generated using the two-way pseudo-testcross approach from 252 individuals. QTL analysis revealed four genomic regions involved in crown rust resistance. Two QTLs were located on LG1 (LpPc4 and LpPc2) and two on LG2 (LpPc3 and LpPc1). They explain 12.5, 24.9, 5.5 and 2.6% of phenotypic variance, respectively. An STS marker, showing homology to R genes, maps in the proximity of LpPc2. Further research is, however, necessary to check the presence of functional R genes in this region. Synteny at the QTL level between homologous groups of chromosomes within the Gramineae was observed.LG1 and LG2 show homology with group A and B chromosomes of oat on which crown rust-resistance genes have been identified, and with the group 1 chromosomes of the Triticeae, on which leaf rustresistance genes have been mapped. These results are of major importance for understanding the molecular background of crown rust resistance in ryegrasses. The identified markers linked to crown rust resistance have the potential for use in marker-assisted breeding. Heredity (2005) 95, 348-357.

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An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Cited by 210 publications

References 53 publications

Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

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